Ensembl Genomes: extending Ensembl across the taxonomic space

Ensembl Genomes (http://www.ensemblgenomes.org) is a new portal offering integrated access to genome-scale data from non-vertebrate species of scientific interest, developed using the Ensembl genome annotation and visualisation platform. Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. Many of the databases supporting the portal have been built in close collaboration with the scientific community, which we consider as essential for maintaining the accuracy and usefulness of the resource. A common set of user interfaces (which include a graphical genome browser, FTP, BLAST search, a query optimised data warehouse, programmatic access, and a Perl API) is provided for all domains. Data types incorporated include annotation of (protein and non-protein coding) genes, cross references to external resources, and high throughput experimental data (e.g. data from large scale studies of gene expression and polymorphism visualised in their genomic context). Additionally, extensive comparative analysis has been performed, both within defined clades and across the wider taxonomy, and sequence alignments and gene trees resulting from this can be accessed through the site.

Estimation of ejection fraction and stroke volume using single- and biplane magnetic resonance imaging of the left cardiac ventricle

BACKGROUND

In cardiac magnetic resonance imaging (MRI), left ventricular stroke volume (SV) and ejection fractions (EF) are occasionally calculated using single-plane and biplane ellipsoid models. In previous studies, the calculated SV and EF using single- and biplane ellipsoid models have been compared to reference values calculated from short-axis (SA) images. In these studies, however, it has been emphasized that through-plane motion of the basal SA images represents an important source of error, which may result in incorrect reference values.

PURPOSE

To compare the calculated SV and EF using single-plane and biplane ellipsoid models with SV and EF calculated from SA images in which compensation was made for through-plane motion.

MATERIAL AND METHODS

A group of 20 patients who underwent MRI examination were included in the study. SV and EF were calculated using the stack of SA images (which had been compensated for through-plane motion) and compared to the SV and EF calculated according to the single- and biplane ellipsoid models.

RESULTS

The mean difference between the single-plane model and the reference was -0.3+/-6.5 for EF and 7.2+/-17.1 ml for SV. Corresponding comparison between the biplane method and the reference resulted in a mean difference of 0.3+/-6.1 for EF and 11.8+/-14.9 ml for SV.

CONCLUSION

The results from this study show that left ventricular EF can be adequately estimated using the single- and biplane ellipsoid models, while SV tends to be overestimated using both geometrical models.

Ensembl 2008

The Ensembl project (http://www.ensembl.org) is a comprehensive genome information system featuring an integrated set of genome annotation, databases and other information for chordate and selected model organism and disease vector genomes. As of release 47 (October 2007), Ensembl fully supports 35 species, with preliminary support for six additional species. New species in the past year include platypus and horse. Major additions and improvements to Ensembl since our previous report include extensive support for functional genomics data in the form of a specialized functional genomics database, genome-wide maps of protein–DNA interactions and the Ensembl regulatory build; support for customization of the Ensembl web interface through the addition of user accounts and user groups; and increased support for genome resequencing. We have also introduced new comparative genomics-based data mining options and report on the continued development of our software infrastructure.

Outer contour and radial changes of the cardiac left ventricle

Earlier studies have shown a +/-5% end-systolic decrease in the volume encompassed by the pericardial sack, manifesting as a radial diminution of the pericardial/epicardial contour of the left ventricle (LV). The aim of this study was to measure this radial displacement at different segmental levels of the LV and try to find out were it is as greatest and to calculate regional myocardial volume changes as a reference in healthy subjects. Eleven healthy subjects were examined by magnetic resonance imaging. Images were acquired using an ECG-triggered balanced fast field echo pulse sequence. The epicardial borders of the LV wall were delineated in end-diastole (ED) and end-systole (ES). Regional changes of the LV wall were analysed at three different levels (base, mid and apex) by dividing the myocardium into segments. The volumes obtained as the differences between the outer volume of the left ventricle at ED and ES at different slice levels were found to be greatest at the base of the heart and lowest at apex. The relative inward motion, that is the motion in short-axis direction of the epicardial border of the myocardium from ED to ES towards the centre of the LV, was greatest at the base and lowest at the mid level, something that has to be taken into account when measuring the LV during clinical exams. There was a significant difference in the relative inward motion between the segments at apex (p < 0.0001), mid (p = 0.036) and at base level (p < 0.0001).

Ensembl 2006

The Ensembl () project provides a comprehensive and integrated source of annotation of large genome sequences. Over the last year the number of genomes available from the Ensembl site has increased from 4 to 19, with the addition of the mammalian genomes of Rhesus macaque and Opossum, the chordate genome of Ciona intestinalis and the import and integration of the yeast genome. The year has also seen extensive improvements to both data analysis and presentation, with the introduction of a redesigned website, the addition of RNA gene and regulatory annotation and substantial improvements to the integration of human genome variation data.

Comparison between circumflex artery motion and mitral annulus motion

OBJECTIVE

To compare mitral annulus motion (MAM) with circumflex artery motion (CXM) and the motion amplitude at an endocardial site (representing MAM) with an epicardial site (representing CXM) at the most basal lateral part of the atrioventricular plane (AVP).

DESIGN

MAM and CXM were obtained in 28 patients examined by echocardiography and coronary angiography. The motion amplitude epicardially and endocardially was recorded by echocardiography in 13 patients with normal ejection fraction (EF) (> or = 0.50) and in 13 patients with decreased EF (<0.50).

RESULTS

CXM was higher than MAM in most patients with normal EF but lower than MAM in most patients with decreased EF. The motion amplitude epicardially was significantly higher (p < 0.001) than endocardially in patients with normal EF. while there was no significant difference in patients with decreased EF.

CONCLUSION

CXM represents the motion of the epicardial part of the AVP and differs from MAM, which represents the endocardial part of the wall. This must be considered when CXM is used for assessment of left ventricular systolic function.

Usefulness of coronary angiography for assessing left ventricular function

The correlation of ejection fraction to left ventricular long-axis contractions, measured from left coronary ostium to apical arterial branches, on coronary angiograms was investigated.